1 Introduction
Introduction to Metabolon: * What is Metabolon? * What do they provide their customers (types of analysis).
Limitations of results from metabolon. * Metabolon uses proprietary source code * Additional quality control * Further exploration * Customized analysis * Many plots to sort through * Subpathway hypothesis testing
Introduction to MetabolomomicsPipeline: * Provides users with the tools for an end to end workflow for the analysis of Metabolon data.
Uses common data structures to allow for easy integration with preexisting genomic pipelines.
Pairwise comparisons for metabolites which can handle differing experimental designs.
Interactive plotting to help identify metabolites of interest.
R package can be utilized through an R shiny wrapper
Picture of workflow
2 Background
Some packages on interactive graphics include plotly (Sievert 2020) that interfaces with Javascript for web-based interactive graphics, crosstalk (Cheng and Sievert 2021) that specializes cross-linking elements across individual graphics. The recent R Journal paper tsibbletalk (Wang and Cook 2021) provides a good example of including interactive graphics into an article for the journal. It has both a set of linked plots, and also an animated gif example, illustrating linking between time series plots and feature summaries.
3 Customizing tooltip design with ToOoOlTiPs
ToOoOlTiPs is a packages for customizing tooltips in interactive graphics, it features these possibilities.
4 A gallery of tooltips examples
The palmerpenguins data (Horst et al. 2020) features three penguin species which has a lovely illustration by Alison Horst in Figure 1.
Figure 1: Artwork by @allison_horst
Table 1 prints at the first few rows of the penguins data:
| species | island | bill_length_mm | bill_depth_mm | flipper_length_mm | body_mass_g | sex | year |
|---|---|---|---|---|---|---|---|
| Adelie | Torgersen | 39.1 | 18.7 | 181 | 3750 | male | 2007 |
| Adelie | Torgersen | 39.5 | 17.4 | 186 | 3800 | female | 2007 |
| Adelie | Torgersen | 40.3 | 18.0 | 195 | 3250 | female | 2007 |
| Adelie | Torgersen | NA | NA | NA | NA | NA | 2007 |
| Adelie | Torgersen | 36.7 | 19.3 | 193 | 3450 | female | 2007 |
| Adelie | Torgersen | 39.3 | 20.6 | 190 | 3650 | male | 2007 |
Figure 2 shows an interactive plot of the penguins data, made using the plotly package.
p <- penguins %>%
ggplot(aes(x = bill_depth_mm, y = bill_length_mm,
color = species)) +
geom_point()
ggplotly(p)Figure 2: A basic interactive plot made with the plotly package on palmer penguin data. Three species of penguins are plotted with bill depth on the x-axis and bill length on the y-axis. When hovering on a point, a tooltip will show the exact value of the bill depth and length for that point, along with the species name.
5 Summary
We have displayed various tooltips that are available in the package ToOoOlTiPs.
5.1 CRAN packages used
plotly, crosstalk, tsibbletalk, palmerpenguins, ggplot2
5.2 CRAN Task Views implied by cited packages
Phylogenetics, Spatial, TeachingStatistics, TimeSeries, WebTechnologies